Marine Microbial Bioprospecting 11.3 Methods for Microbial Bioprospecting in Marine Environments 315
Part B | 11.3
Institute created the initiative Genomic Encyclopedia
of Bacteria and Archaea (Table 11.2). Similarly, the
Microbial Genome Sequencing Project of the Gordon
and Betty Moore Foundation’s Marine Microbiology
Initiative has sequenced the genome of hundreds of ecologically relevant microorganisms isolated from diverse
marine habitats (Table 11.2).
The phenotypic analysis of isolates can severely
underestimate its genetic potential, as genes may not
be expressed or may be expressed at very low levels under laboratory conditions. For example, it has
been proposed that a unique combination of environmental factors may be required for the expression of
biosynthetic genes [11.6]. Therefore, the mining for
genes or gene clusters in microbial genomes could
uncover hidden treasures that could be exploited, for
example, using heterologous gene expression [11.90].
Moreover, the use of sequence information has assisted
in the determination of the chemical structure of new
compounds by a combination of bioinformatics and
chemistry [11.91]. The potential for biodiscovery of
this approach has led to the explosion of interest in
genome mining as a tool for bioprospection, which has
been aided by the development of new bioinformatic
tools for the analysis of the growing volume of DNA
sequence data [11.92]. However, as sequencing efforts
are rarely followed by the biochemical characterization
of the putative gene products, many genes emerging
from these studies have unknown functions, and basic local alignment search tool (BLAST)-based protein
functional assignments can easily propagate annotation
errors [11.93]. Recently, a database of experimentally
characterized proteins was created (CharProtDB, Table 11.2), enabling to link experimental characterizations of protein functions with computationally accessible protein sequences [11.94].
The mining of the ever-increasing amount of genomic data from marine microorganisms has led to
the bioassay-independent discovery of gene clusters
with important biotechnological applications [11.95].
In recently published work, Wargacki and collaborators [11.96] used a public database to identify a genome
fragment from the Vibrio splendidus strain 12B01, containing genes for alginate degradation, transport, and
metabolism. This gene cluster was used to construct
a microbial platform that enables bioethanol production
from macroalgae via a consolidated process [11.96].
In silico mining of genomes combined with molecular biology approaches has resulted in the discovery
of novel gene clusters with potential use for the development of peptide-based drug candidates [11.95].
In addition, a search of sequenced bacterial genomes
showed that marine cyanobacteria present an extraordinarily efficient strategy for generating many cyclic
peptide secondary metabolites [11.97].
Other Omics Approaches
Currently, only one-third of an annotated bacterial genome corresponds to information that is well
known [11.98]. However, in order to understand how
a cell operates and, therefore, for the successful application of its genetic potential, a better knowledge
of the two ignored parts is required. Molecular approaches that can be used in combination with genome
sequencing to study a marine microbial isolate include, for instance, transcriptomics, proteomics, and
metabolomics [11.99]. Concerning transcriptomics, the
development first of microarray technology and later
of whole transcriptome shotgun sequencing using nextgeneration sequencing technologies has provided valuable insight into gene function and regulation [11.100].
Importantly, this information also serves as a basis for
genome re-annotation. In addition to its function as information carrier, RNA can present various regulatory
functions in bacteria [11.101]. Although this information is still in its infancy, it could be highly valuable for
the biotechnological application of pure cultures.
Technological advances in the field of mass spectrometry (MS) have enabled us to obtain information
regarding a significant proportion of the proteome of
microbial isolates [11.102]. Several proteomic studies
of cyanobacterial strains have been published, which
are microorganisms that have interesting biotechnological applications [11.103]. For example, the analysis of the proteome of Synechocystis sp. PCC 6803
rendered evidence of the mechanisms used by this
microorganism for gaining resistance against the biofuel hexane [11.104]. In a second study, the complex response of this model microorganism to ethanol
was analyzed using a quantitative proteomics approach [11.105]. Ethanol sensitivity of cyanobacteria
currently restricts efforts to increase biofuel production
levels in metabolic engineered strains for autotrophic
ethanol production, and this study provided a list of potential gene targets for engineering ethanol tolerance.
Although highly challenging due to the extremely
fast turnover times of the small molecules of the cell,
metabolomics is fundamental for the understanding
of metabolic reaction networks and their regulation,
as well as to link the genotype of an isolate to its
phenotype [11.106]. Interactomics, on the other hand,
attempts to resolve the whole set of molecular in-
Part B | 11.3
Institute created the initiative Genomic Encyclopedia
of Bacteria and Archaea (Table 11.2). Similarly, the
Microbial Genome Sequencing Project of the Gordon
and Betty Moore Foundation’s Marine Microbiology
Initiative has sequenced the genome of hundreds of ecologically relevant microorganisms isolated from diverse
marine habitats (Table 11.2).
The phenotypic analysis of isolates can severely
underestimate its genetic potential, as genes may not
be expressed or may be expressed at very low levels under laboratory conditions. For example, it has
been proposed that a unique combination of environmental factors may be required for the expression of
biosynthetic genes [11.6]. Therefore, the mining for
genes or gene clusters in microbial genomes could
uncover hidden treasures that could be exploited, for
example, using heterologous gene expression [11.90].
Moreover, the use of sequence information has assisted
in the determination of the chemical structure of new
compounds by a combination of bioinformatics and
chemistry [11.91]. The potential for biodiscovery of
this approach has led to the explosion of interest in
genome mining as a tool for bioprospection, which has
been aided by the development of new bioinformatic
tools for the analysis of the growing volume of DNA
sequence data [11.92]. However, as sequencing efforts
are rarely followed by the biochemical characterization
of the putative gene products, many genes emerging
from these studies have unknown functions, and basic local alignment search tool (BLAST)-based protein
functional assignments can easily propagate annotation
errors [11.93]. Recently, a database of experimentally
characterized proteins was created (CharProtDB, Table 11.2), enabling to link experimental characterizations of protein functions with computationally accessible protein sequences [11.94].
The mining of the ever-increasing amount of genomic data from marine microorganisms has led to
the bioassay-independent discovery of gene clusters
with important biotechnological applications [11.95].
In recently published work, Wargacki and collaborators [11.96] used a public database to identify a genome
fragment from the Vibrio splendidus strain 12B01, containing genes for alginate degradation, transport, and
metabolism. This gene cluster was used to construct
a microbial platform that enables bioethanol production
from macroalgae via a consolidated process [11.96].
In silico mining of genomes combined with molecular biology approaches has resulted in the discovery
of novel gene clusters with potential use for the development of peptide-based drug candidates [11.95].
In addition, a search of sequenced bacterial genomes
showed that marine cyanobacteria present an extraordinarily efficient strategy for generating many cyclic
peptide secondary metabolites [11.97].
Other Omics Approaches
Currently, only one-third of an annotated bacterial genome corresponds to information that is well
known [11.98]. However, in order to understand how
a cell operates and, therefore, for the successful application of its genetic potential, a better knowledge
of the two ignored parts is required. Molecular approaches that can be used in combination with genome
sequencing to study a marine microbial isolate include, for instance, transcriptomics, proteomics, and
metabolomics [11.99]. Concerning transcriptomics, the
development first of microarray technology and later
of whole transcriptome shotgun sequencing using nextgeneration sequencing technologies has provided valuable insight into gene function and regulation [11.100].
Importantly, this information also serves as a basis for
genome re-annotation. In addition to its function as information carrier, RNA can present various regulatory
functions in bacteria [11.101]. Although this information is still in its infancy, it could be highly valuable for
the biotechnological application of pure cultures.
Technological advances in the field of mass spectrometry (MS) have enabled us to obtain information
regarding a significant proportion of the proteome of
microbial isolates [11.102]. Several proteomic studies
of cyanobacterial strains have been published, which
are microorganisms that have interesting biotechnological applications [11.103]. For example, the analysis of the proteome of Synechocystis sp. PCC 6803
rendered evidence of the mechanisms used by this
microorganism for gaining resistance against the biofuel hexane [11.104]. In a second study, the complex response of this model microorganism to ethanol
was analyzed using a quantitative proteomics approach [11.105]. Ethanol sensitivity of cyanobacteria
currently restricts efforts to increase biofuel production
levels in metabolic engineered strains for autotrophic
ethanol production, and this study provided a list of potential gene targets for engineering ethanol tolerance.
Although highly challenging due to the extremely
fast turnover times of the small molecules of the cell,
metabolomics is fundamental for the understanding
of metabolic reaction networks and their regulation,
as well as to link the genotype of an isolate to its
phenotype [11.106]. Interactomics, on the other hand,
attempts to resolve the whole set of molecular in-