Open Access is an initiative that aims to make scientific research freely available to all. To date our community has made over 100 million downloads. It’s based on principles of collaboration, unobstructed discovery, and, most importantly, scientific progression. As PhD students, we found it difficult to access the research we needed, so we decided to create a new Open Access publisher that levels the playing field for scientists across the world. How? By making research easy to access, and puts the academic needs of the researchers before the business interests of publishers.
We are a community of more than 103,000 authors and editors from 3,291 institutions spanning 160 countries, including Nobel Prize winners and some of the world’s most-cited researchers. Publishing on IntechOpen allows authors to earn citations and find new collaborators, meaning more people see your work not only from your own field of study, but from other related fields too.
Genetic transformation is a powerful tool not only for elucidating the functions and regulatory mechanisms of genes involved in various physiological events but also for establishing organisms that efficiently produce biofuels and medically functional materials or carry stress tolerance in face of uncertain environmental conditions (Griesbeck et al., 2006; Torney et al., 2007; Bhatnagar-Mathur et al., 2008). Eukaryotic algae classified into microalgae and macroalgae (seaweeds) are highly diverse photosynthetic plants that are utilized as human food and animal feed as well as sources of valuable compounds such as fatty acids, pigments, vitamins and polysaccharides (Hallmann, 2007; Sugawara et al, 2011). Because of their importance in ecology and industry, algae are now considered promising organisms for economical and industrial applications and are thus a target of genetic transformation (Walker et al., 2005; Hallmann, 2007; Blouin et al., 2011). To date, genetic transformation has succeeded in microalgae; thus, stably transformed microalgae are now employed to produce recombinant antibodies, vaccines, or bio-hydrogen as well as to analyze the gene functions targeted for engineering (Sun et al., 2003; Zorin et al., 2009; Specht et al., 2010; Wu et al., 2010). However, it has proven difficult to establish transgenic macroalgae, which has hampered understanding their gene functions in various physiological regulations and also their utilization in biotechnological applications.
The red macroalga Porphyra yezoensisis the most popular sea crop in Japan with economical and pharmaceutical importance as the source of foods such as “nori” and pharmacological regents such as the sulfated polysaccharide “porphyran”, which has anti-tumor and anti-allergic activities (Noda et al., 1990; Zemke-White & Ohno, 1999; Ishihara et al., 2005). Recently, non-beneficial climate change due to global warming has decreased the quality and yield of P. yezoensisat algal farms by enhancing discoloration and red rot disease caused by fungal infection (Kakinuma et al., 2008; Park et al., 2000). Although breeding of P. yezoensisby traditional selection and crossing methods has progressed to obtain strains showing high growth rates and economically valuable characteristics, these methods have limitations in terms of the isolation of strains carrying heat-stress tolerance or disease resistance. Development of a molecular breeding method based on genetic transformation is expected to resolve this problem using knowledge about gene functions in P. yezoensis.
Despite the difficulty of genetic transformation, genetic information about P. yezoensisis now accumulating by a collection of ESTs from leafy gametophytes and filamentous sporophytes (Nikaido et al., 2000; Asamizu et al., 2003) and also by ongoing full-length cDNA and whole genome analyses. Genetic information provides a sophisticated way to isolate P. yezoensisgenes of interest; however, utilization of this knowledge – in both basic biological research and molecular breeding of P. yezoensis– is hindered by the lack of a genetic transformation system.
Given this situation, it is clear that the development of a genetic transformation system for P. yezoensisis critical for sustainable production as well as the enhancement of biological study. In our laboratory much effort has been expended on the establishment of a genetic transformation system; as a result we have identified several factors preventing the establishment of a genetic transformation system in macroalgae: for example, the lack of efficient methods for foreign gene transfer and expression systems and the absence of valid selectable markers for isolation of genetically transformed cells. Thus, it is considered worthwhile to develop a transient gene expression system, because some of the above inhibiting factors, such as defects in the transfer and expression of foreign genes, could be removed by using non-integrated plasmids containing genes for expression. Since we have recently succeeded in developing an efficient transient gene expression system in Bangiophyceae including Porphyraspecies, the establishment and successful application of this system in a molecular biological study are summarized here.
2. Development of a transient gene expression system in P. yezoensiscells
2.1. Problems in previously published experiments
Expression of foreign genes in macroalgae has already been attempted using bacterial lacZ(β-galactosidase) and uidA(β-glucronidase, GUS) genes under direction by promoters of the cauliflower mosaic virus 35S RNA (CaMV 35S) and simian virus 40 (SV40) genes (Kübler et al., 1994; Kuang et al., 1998; Huang et al., 1996; Gan et al., 2003; Jiang et al., 2003). The CaMV 35Sand SV40promoters are typical eukaryotic class II promoters with a TATA box and thus are generally employed to drive transgenes in dicot plant and animal cells, respectively (Kang & An, 2005; Funabashi et al., 2010). However, we have observed a quite low activity of the CaMV 35Spromoter in P. yezoensiscells as shown in Figs. 1 and 2 (Fukuda et al., 2008), which is strongly supported by the fact that the TATA box is not found in the core promoters of P. yezoensisgenes (unpublished observation), suggesting differences in the promoter structure and transcriptional regulation of protein-coding genes between red algae and dicot plants. We believe that the same could be predicted for the SV40 promoter. Thus, it seems to be necessary to reconfirm the results of reporter expression using the CaMV 35Sand SV40promoters in red algae like P. miniata, P. tenera, Kappaphycus alvareziiand Gracilaria changiiin previously published literatures (Kurtzman & Cheney, 1991; Kübler et al., 1994; Okauchi & Mizukami, 1999; Cheney et al., 2001; Gan et al., 2003).
In addition, the use of the GUSreporter gene is also a problem, since we have already confirmed that the GUSreporter gene is not functional in red algal cells by histochemical analysis and enzymatic activity test (see below). This is supported by previous reports indicating background levels of the GUS enzymatic activity in red and brown macroalgal cells when the GUS reporter gene was driven by CaMV 35Sand endogenous beta-tubulin promoters (Liu et al., 2003; Gong et al., 2005).
According to the above findings, previous reports of successful expression of the GUSreporter gene under the direction of the CaMV 35Sand SV40promoters are not likely to be replicated. Thus, an important step is to enable the effective expression of the GUSreporter genes in P. yezoensiscells, which should eventually lead to the establishment of a transient gene expression system via the development of procedures for introduction and expression of foreign genes as described below.
2.2. Codon-optimization of the reporter gene
Inefficient expression of foreign genes in algal cells is often due to the incompatibility of the codon usage in their coding regions, inhibiting the effective use of transfer RNA by rarely used codons in the host cells and thus decreasing the efficiency of the translation (Mayfield & Kindle, 1990). In this respect, successful development of foreign gene expression in green alga Chlamydomonas reinhardtiimay be an important clue to overcoming the deficiency of the GUS reporter gene in P. yezoensiscells. For example, a low expression level of the gene encoding a green fluorescent protein (GFP) from the jellyfish Aequorea victoria, whose codon usage is rich in AT residues, was dramatically increased by adjustment of the GC content of the coding region corresponding to the codon usage in C. reinhardtiinuclear genes (Fuhrmann et al., 1999). In addition, the synthetic luciferase gene whose codon usage was adapted to that in nuclear genes from C. reinhardtiiwas also expressed efficiently, although the original luciferase gene had less efficiency in C. reinhardtiicells (Fuhrmann et al., 2004; Ruecker et al., 2008; Shao & Bock, 2008). In fact, EST analysis of P. yezoensisreveals that the codons in P. yezoensisnuclear genes frequently contain G and C residues especially in their third letters, by which the GC content reaches a high of 65.2% (Nikaido et al., 2000). Since bacterial GUSand lacZreporter genes have AT-rich codons, the incompatibility of codon usage might be responsible for the poor translation efficiency of foreign genes in P. yezoensiscells. We therefore postulated that modification of codon usage in the GUSgene would enable the efficient expression of this gene in P. yezoensiscells. This possibility led us to modify the codon usage of the GUS reporter gene to that in the nuclear genes of P. yezoensisby introducing silent mutations in the GUS coding region, by which unfavorable or rare codons in the GUS reporter gene were exchanged for favorable ones without affecting amino acid sequences. In the resultant artificially codon-optimized GUS gene, designated PyGUS, the GC content was increased from 52.3% to 66.6%.
To transfer the plasmid into cells, we employed particle bombardment, also referred to as micro-projectile bombardment, particle guns, or biolistics, which are among the most popular techniques for achieving nuclear and organelle transformation not only for algae but also for plants, fungi, insects, animals and even bacteria. In this method, DNA-coated heavy-metals, usually gold or tungsten particles, are introduced into cells by helium pressure, which enables the introduction of foreign DNA regardless of whether the cell has a cell wall. This method has been successfully applied in many algal species such as C. reinhardtii(Kindle et al., 1989), Volvox carteri(Schiedlmeier et al., 1994), Dunaliella salina(Tan et al., 2005), and Phaeodactylum tricornutum(Apt et al., 1996).
When the PyGUSgene directed by the CaMV 35Spromoter was introduced into P. yezoensisgametophytic cells by particle bombardment, very low but significant expression of the PyGUSgene was observed by histochemical detection and GUS activity test (Figs. 1 and 2), indicating the enhancement of the expression level of the GUSreporter gene. Optimization of the codon usage of the reporter gene is therefore one of the important factors for successful expression in P. yezoensiscells (Fukuda et al., 2008; Mikami et al., 2009; Takahashi et al., 2010; Uji et al., 2010; Hirata et al., 2011).
2.3. Employment of an endogenous strong promoter
A low level of PyGUSexpression under the direction of the CaMV 35Spromoter was thought to be caused by the low activity of this promoter in P. yezoensiscells. Although the CaMV 35Spromoter is widely used as a heterologous promoter because of its strong, constitutive and non-tissue-specific transcriptional function in dicot plant cells (Louis et al., 2010; Wally & Punja, 2010), it is well known that this promoter has very low activity in cells of green algae such as Dunaliella salina(Tan et al., 2005), Chlorella kessleri(El-Sheekh, 1999), and Chlorella vulgaris(Chow & Tung, 1999) and no activity in C. reinhardtiicells (Day et al., 1990; Blakenship & Kindle, 1992; Lumbreras et al., 1998). However, employment of strong endogenous promoters such as the β-Tub, RbcS2and Hsp70promoters has achieved efficient expression of foreign genes in these algae (Davies et al., 1992; Stevens et al., 1996; Schroda et al., 2000; Walker et al., 2004). In addition, many endogenous promoters have been developed and successfully used for foreign gene expression in cells of some microalgae, such as the diatom Phaeodactylum tricornutumand the Chlorarachniophyte Lotharella amoebiformis(Zaslavskaia et al., 2000; Hirakawa et al., 2008). Therefore, it is possible that recruitment of suitable strong promoters could result in efficient expression of the PyGUSreporter gene in P. yezoensiscells.
Since we found strong expression of P. yezoensisgenes encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and actin 1 (Act1) by reverse transcription-PCR (RT-PCR) (see Fig. 5), the 5’ upstream regions of these genes were isolated from the P. yezoensisgenome and fused with the PyGUSgene to construct the expression plasmids pPyGAPDH-PyGUS and pPyAct1-PyGUS in addition to the pPyGAPDH-GUS and pPyAct1-GUS plasmids. When pPyGAPDH-GUS and pPyGAPDH-PyGUS were introduced into gametophytic cells by particle bombardment, cells expressing the reporter gene and GUS enzymatic activity were dramatically increased using the PyGUSgene as a reporter, although the original GUSgene was not efficiently expressed (Figs. 1 and 2). The same results were obtained using pPyAct1-PyGUS and pPyAct1-GUS plasmids (Figs. 1 and 2). Thus, the combination of endogenous strong promoters with codon optimization brings a synergistic effect on the efficiency of the expression of the reporter gene. These results indicate that employment of an endogenous strong promoter is another important factor necessary for high-level expression of the reporter gene in P. yezoensiscells (Fukuda et al., 2008).
It is noteworthy that significant expression of PyGUS under the direction of the PyAct1and PyGAPDHpromoters was also observed in sporophytic cells in P. yezoensis, when the expression plasmid was introduced using particle bombardment (Fig. 3A). However, the PyGUS enzymatic activity was much lower than those in gametophytic cells (Fig. 3B). This difference was thought to be mainly due to the difference in DNA-transferring efficiency based on the difficulty of targeting the cell for gene transfer in sporophytes of thin filamentous form by particle bombardment.
Our transient gene expression system with the above methodological imorovement is represented schematically in Fig. 4.
2.4. Evaluation of gene transfer methods
Our initial development of transient expression of the PyGUSreporter gene in P. yezoensiscells depended on the use of particle bombardment, in which the gene transfer rate was usually 103 per μg of DNA. However, it is necessary to increase the efficiency of the foreign gene expression to 106 to 107 per μg of DNA, because the establishment of a genetic
transformation system requires a large number of gene-transferred cells, a small portion of which are stably transformed by integration of the foreign gene into the genome. Thus, it is important to develop an efficient method of gene transfer into P. yezoensiscells toward the establishment of a stable transformation system via genetic recombination. However, our preliminary experiments with the glass beads method (Kindle, 1990; Feng et al., 2009), PEG method (Ohnuma et al., 2008) and magnetofection (Plank et al., 2003; Svingen et al., 2009) resulted in failure to introduce foreign genes into P. yezoensis. Thus, particle bombardment appears to be the only method available for transferring foreign genes into P. yezoensiscells at present, and further development of a gene transfer method to acheive very high efficient expression of the PyGUSreporter gene is required.
In fact, there have been several reports on DNA transfer into Porphyracells using electroporation (Kübler et al., 1994) and Agrobacterium-mediated transformation (Cheney et al., 2001). Although the experiments in these reports had problems in the efficiency of the reporter gene expression based on the use of the CaMV 35Spromoter and original GUSreporter gene, they are valuable as points of comparison for the increase in efficiency of gene transfer and expression by using, for example, the PyAct1-PyGUSor PyGAPDH-PyGUSreporter gene.
3. Application of the transient gene expression
3.1. Promoter analysis by PyGUS reporter system
Elucidation of the regulatory mechanisms of gene expression is crucial to understanding the molecular mechanisms governing plant stress responses, leading to enhancement of stress tolerance in plants through genetic transformation (Shinozaki & Yamaguchi-Shinozaki, 2007; Bhatnagar-Mathur et al., 2008). The transient gene expression system has been successfully applied to analyze promoters of stress-inducible genes to identify stress-responsible cis-regulatory elements in higher plants. For example, cold- and drought-responsible elements have been identified using the GUS reporter system in barley and Arabidopsis thaliana(Brown et al., 2001; Sakamoto et al., 2004). These successes are based on the quantitative correlation between promoter strength and reporter gene expression. Confirmation of this point in the transient gene expression system is indispensable for further analysis of stress-inducible genes in P. yezoensis.
To check the correlation between the promoter strength and expression level of the PyGUS reporter in P. yezoensiscells, mRNA expression levels of the actin 1 (PyAct1), GAPDH (PyGAPDH), Na+-ATPase (PyATP1A) and transcription elongation factor 1 (PyElf1) genes were compared with PyGUS enzymatic activities derived from expression plasmids of the PyGUSgene under the direction of these promoters. The result indicated a strong correlation between the mRNA levels of these genes analyzed by RT-PCR and GUS enzymatic activities via expression of the PyGUS reporter gene directed by the corresponding promoter (Fig. 5), demonstrating the applicability of our transient gene expression system with the PyGUSgene to promoter analyses of P. yezoensisgenes. Identification of cis-regulatory elements by promoter analysis is now underway for stress-inducible genes using the transient PyGUS reporter expression system.
3.2. Development of fluorescent protein reporter system
Since histochemical and quantitative enzymatic analyses in the PyGUS reporter system require cell killing, monitoring of the reporter expression during development or response to environmental stress in living cells is impossible to analyze. However, living cell imaging to monitor gene expression is possible using fluorescent proteins without additional substrates and cofactors (Ehrhardt, 2003). Indeed, fluorescent proteins are usually employed as useful tools to visualize protein localization in living cells in land plants (Buschmann et al., 2010; Kokkirala et al., 2010; Meng et al., 2010; Pribat et al., 2010).
We first examined the usability of fluorescent proteins as reporters in P. yezoensiscells, since the expression of fluorescent protein has not yet been demonstrated in red algal cells. Table 1 lists fluorescent protein genes such as green fluorescent protein (GFP) and its variants cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) from various organisms including the jellyfish Aequorea victoria, reef coral Zoanthussp. and copepoda Pontellina plumata, whose codon usage is biased to be GC-rich by humanization. When these genes were expressed in P. yezoensiscells under the direction of the PyAct1promoter, a fluorescent signal was clearly observed in every transiently transformed cell. Fig. 6A represents the expression of AmCyan and ZsGreen as examples. Interestingly, the gene encoding plant-adapted GFP(S65T) (Niwa et al., 1999) under the direction of the PyAct1promoter also produced the GFP signal (Fig. 6A). Since the GC contents of humanized fluorescent proteins and sGFP(S65T) are as high as 60% (Table 1), a GC content of 60% appears to be sufficient for efficient expression of foreign genes in P. yezoensiscells.
Applicability of the fluorescent protein system to visualize protein localization in P. yezoensiscells has already been demonstrated. For example, as shown in Fig. 6B, plasma membrane localization of Pleckstrin homology (PH) domains from human phospholipase Cδ1 was demonstrated using AmCyan (Mikami et al., 2009) and nuclear localization of P. yezoensistranscription factor PyElf1 was also confirmed using AmCyan and ZsGreen (Uji et al., 2010). Thus, these applications will provide new opportunities for analyzing subcellular localization of various genes from P. yezoensis.
3.3. Application of PyGUS and sGFP(S65T) reporter systems in other red macroalgae
Since red macroalgae include a number of industrially important species such as Porphyraas the source of the food known as Nori, Gracilariaand Gelidiumas sources of agar and Chondrusand Kappaphycusas sources of carrageenan, the establishment of a genetic manipulation system for these algae is eagerly anticipated. However, a transient gene expression system has not yet been developed in these red macroalgae other than P. yezoensis. In fact, EST analysis of P. haitanensisrevealed that the GC content of the ORFs in this alga was as high as that in P. yezoensis, and the GC content at the third position of the triplets was significantly higher than those at the other two positions, which is consistent with the result reported in P. yezoensis(Fan et al., 2007). Similarly, analysis of the GAPDHgene from Chondrus crispusshowed a high GC content (approximately 60%) in the cording region (Liaud et al., 1993). Thus, it is possible that the PyGUSgene could be commonly functional in red algae as a reporter of the gene expression. Indeed, applicability of the PyGUSgene in P. tenerahas recently been confirmed by another laboratory (Son et al., 2011).
The applicability of the P. yezoensistransient gene expression system was examined using the PyGUS and sGFP(S65T) reporter genes under the direction of the PyAct1promoter in the red macroalgae listed in Table 2. Good expression of PyGUS and sGFP(S65T) was observed in Bangiophyceae including genus Porphyraand Bangia, whereas no expression of the reporter genes was seen in Florideophyceae (Table 2). Thus, it was concluded that the transient gene expression system developed in P. yezoensisis widely applicable in Bangiophycean red algae (Hirata et al., 2011).
The number of reporter-expressing cells varies among species (Table 2; Hirata et al., 2011), suggesting the possibility of the improvement of the gene transfer and expression systems in each species using respective endogenous strong promoters to drive the expression of the PyGUS and the sGFP(S65T) reporter genes. Similarly, expression of these reporter genes in Florideophycean algae seems to be possible if suitable endogenous promoters can be employed. Establishment of an efficient transient gene expression system will stimulate future development of stable transformation systems in various red macroalgae, enabling more effective utilization of them for industrial purposes.
Genetic transformation is indispensable both to elucidation of gene function and to molecular breeding of crop plants. Our major goal is to establish a stable transformation system to produce Porphyraspecies carrying biotic and abiotic stress tolerances. For this purpose, our recent development of a transient gene expression system for Bangiophycean algae, by which the lack of transfer and expression systems for foreign genes was resolved, is the first breakthrough toward the establishment of a genetic transformation method in red macroalgae. We now know that the construction of an expression plasmid requires both optimization of codon usage in coding regions of the reporter gene and recruitment of endogenous strong promoters; also that particle bombardment is the proven method of gene transfer into red algal cells. The next steps are therefore development of targeted or random integration systems of foreign genes into the genome and selection of marker genes useful for isolation of transformed cells. Resolution of these methodological problems could contribute to accelerating progress in molecular biological research on physiological regulations that will be useful for the industrial production of transgenic red macroalgae.
This work was suported in part by a grant from the Regional Innovation Cluster Program (Global Type) from the Ministry of Education, Culture, Sports, Science, and Technology, Japan to N.S. and the Hokusui Foundation to K.M.
A Recombination Puzzle Solved: Role for New DNA Repair Systems in Helicobacter pylori Diversity/Persistence
By Ge Wang and Robert J. Maier
We are IntechOpen, the world's leading publisher of Open Access books. Built by scientists, for scientists. Our readership spans scientists, professors, researchers, librarians, and students, as well as business professionals. We share our knowledge and peer-reveiwed research papers with libraries, scientific and engineering societies, and also work with corporate R&D departments and government entities.