@article {439,
	title = {Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.},
	journal = {BMC Evol Biol},
	volume = {10},
	year = {2010},
	month = {2010},
	pages = {230},
	abstract = {BACKGROUND: Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR) separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences.

RESULTS: CRISPR spacer $\#$1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is unlikely to compensate for interference with hisS. Spacer $\#$1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which the native hisS was replaced with that of P. carbinolicus. The prediction that interference with hisS would result in an attenuated histidyl-tRNA pool insufficient for translation of proteins with multiple closely spaced histidines, predisposing them to mutation and elimination during evolution, was investigated by comparative genomics of P. carbinolicus and related species. Several ancestral genes with high histidine demand have been lost or modified in the P. carbinolicus lineage, providing an explanation for its physiological differences from other Geobacteraceae.

CONCLUSIONS: The disappearance of multiheme c-type cytochromes and other genes typical of a metal-respiring ancestor from the P. carbinolicus lineage may be the consequence of spacer $\#$1 interfering with hisS, a condition that can be reproduced in a heterologous host. This is the first successful co-introduction of an active CRISPR spacer and its target in the same cell, the first application of a chimeric CRISPR construct consisting of a spacer from one species in the context of repeats of another species, and the first report of a potential impact of CRISPR on genome-scale evolution by interference with an essential gene.},
	keywords = {Base Sequence, Comparative Genomic Hybridization, Computational Biology, Deltaproteobacteria, DNA, Bacterial, DNA, Intergenic, Evolution, Molecular, Genes, Bacterial, Genome, Bacterial, Geobacillus, Histidine-tRNA Ligase, Inverted Repeat Sequences, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, DNA},
	issn = {1471-2148},
	doi = {10.1186/1471-2148-10-230},
	author = {Aklujkar, Muktak and Lovley, Derek R}
}
@article {461,
	title = {The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens.},
	journal = {BMC Microbiol},
	volume = {9},
	year = {2009},
	month = {2009},
	pages = {109},
	abstract = {BACKGROUND: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences.

RESULTS: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes.

CONCLUSION: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.},
	keywords = {Bacterial Proteins, DNA, Bacterial, Gene Expression Regulation, Bacterial, Genome, Bacterial, Geobacter, Phylogeny, Sequence Analysis, DNA, Species Specificity, Transcription Factors},
	issn = {1471-2180},
	doi = {10.1186/1471-2180-9-109},
	author = {Aklujkar, Muktak and Krushkal, Julia and DiBartolo, Genevieve and Lapidus, Alla and Land, Miriam L and Lovley, Derek R}
}
