Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms

Xu, Lin; Chen, Hong; Xiao-hua, HU; Zhang, Rongmei; Zhang, Ze; Luo, Zongli

doi:10.1093/molbev/msk019

Cited by 118 publications

(114 citation statements)

References 9 publications

Supporting

Mentioning

103

Contrasting

Order By: Relevance

“…The average lengths of ARMAN genes are small (Table 1), compared with the average gene length for most Archaea of 924 bp. This finding is notable, given general conservation of gene length in most Bacteria and Archaea (37). To rule out effects because of genome fragmentation, we verified the small gene size across several large syntenic fragments.…”

Section: Resultsmentioning

confidence: 89%

Enigmatic, ultrasmall, uncultivated Archaea

Baker¹,

Comolli

Dick³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

299

292

View full text Add to dashboard Cite

Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete ∼1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) (1)]. Many datasets provide fragmentary glimpses into genetic diversity (2-4) and a few have reported near-complete genomic sequences for uncultivated organisms (5-8). In most cases where extensive reconstruction has been possible, insights have been restricted to relatively dominant members. Furthermore, it has been difficult to use genomic information to infer the nature of interorganism interactions, although these are likely to be very important aspects of microbial community functioning. The need for topological and organizational information to place genomic data in context motivates the combination of cultivation-independent genomics and 3D cryogenic transmission electron microscope-based ultrastructural analyses of microbial communities.Despite the importance of cellular interactions (symbiosis and parasitism), most of what we know about microorganismal associations is from cultivation-based studies (9-11). However, sequencing of the genomes of several endosymbiotic and parasitic Bacteria has revealed reduction in gene and genome sizes, reflecting evolved dependence of the endosymbiont or parasite on its host (12, 13). The ultrasmall archaeal parasite Nanoarchaeum equitans has only 552 genes and requires a connection to its archaeal host, Ignicoccus hopstialis, to survive (10). Recently, it was shown that this interaction involves contact between outer membranes (14). Given the vast diversity of microbial life (15), it is likely that other unusual relationships critical to surviva...

show abstract

Section: Resultsmentioning

confidence: 89%

Enigmatic, ultrasmall, uncultivated Archaea

Baker¹,

Comolli

Dick³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

299

292

View full text Add to dashboard Cite

show abstract

“…This calculation requires estimates of RNA extraction efficiency (we assumed 50%), the make-up of bacterial RNA (we assumed 4% mRNA by mass; Neidhardt and Umbarger, 1996), and the average length of a bacterial mRNA (we assumed 924 nt; Xu et al, 2006). By this method, bacterioplankton cells in various coastal environments have an average mRNA content of B300 molecules (Table 1), with calculations for freshwaters, soils and sediments likely to be similar.…”

Section: Mrna Content Of Bacterial Cellsmentioning

confidence: 99%

“…Despite the poor correlations between single-cell mRNA and protein abundances observed by Taniguchi et al (2010), their data coalesced into a predictable relationship when averaged across many (Neidhardt and Umbarger, 1996) and bacterial mRNAs have an average length of 924 nucleotides (Xu et al, 2006) and therefore an average weight of 4.72 Â 10 À 4 fg.…”

Section: Correlation Between Mrna and Protein Abundance In A Populationmentioning

confidence: 99%

Sizing up metatranscriptomics

et al. 2012

View full text Add to dashboard Cite

A typical marine bacterial cell in coastal seawater contains only B200 molecules of mRNA, each of which lasts only a few minutes before being degraded. Such a surprisingly small and dynamic cellular mRNA reservoir has important implications for understanding the bacterium's responses to environmental signals, as well as for our ability to measure those responses. In this perspective, we review the available data on transcript dynamics in environmental bacteria, and then consider the consequences of a small and transient mRNA inventory for functional metagenomic studies of microbial communities.

show abstract

“…To synthesize a DNA genome, one can imagine that genes or entire operons would be copied from simple organisms such as bacteria or bacteriophages. Most of the genes in microorganisms are smaller than in higher organisms, and they encode for single-function proteins (64,65).…”

Section: Bottom-up Development Of An Artificial Cell: Broad Consideramentioning

confidence: 99%

Development of an artificial cell, from self-organization to computation and self-reproduction

Noireaux¹,

Maeda

Libchaber

2011

Proc. Natl. Acad. Sci. U.S.A.

292

265

View full text Add to dashboard Cite

This article describes the state and the development of an artificial cell project. We discuss the experimental constraints to synthesize the most elementary cell-sized compartment that can self-reproduce using synthetic genetic information. The original idea was to program a phospholipid vesicle with DNA. Based on this idea, it was shown that in vitro gene expression could be carried out inside cell-sized synthetic vesicles. It was also shown that a couple of genes could be expressed for a few days inside the vesicles once the exchanges of nutrients with the outside environment were adequately introduced. The development of a cell-free transcription/translation toolbox allows the expression of a large number of genes with multiple transcription factors. As a result, the development of a synthetic DNA program is becoming one of the main hurdles. We discuss the various possibilities to enrich and to replicate this program. Defining a program for self-reproduction remains a difficult question as nongenetic processes, such as molecular self-organization, play an essential and complementary role. The synthesis of a stable compartment with an active interface, one of the critical bottlenecks in the synthesis of artificial cell, depends on the properties of phospholipid membranes. The problem of a self-replicating artificial cell is a long-lasting goal that might imply evolution experiments.Defining Life Since Schrödinger's classic book What Is Life? (1), the definition of life has always been a puzzle with a variety of partial answers, none really satisfying. One answer is that life is a coded system with mutation and error correction (2). The information is encoded into DNA (the genotype) and the genetic code allows translating this information into proteins (the phenotype). The genetic code is universal, and the genome can support mutations, recombination, duplication, and partial transfer from organisms to organisms. Error correction limits the risk of melting the information into random sequences. This is fine, but life is also metabolism with a permanent absorption and transformation of nutrients from the environment (3). A constant flux of energy is needed to sustain the operation of this living dynamical system out of equilibrium. But life is also self-reproduction (4). Cells originate from preexisting cells by cell division. The DNA genome is replicated, the cell self-reproduces as well as the complete organism. Is self-reproduction a constraint of evolution present at each step and imposing severe design constraints or a possible definition of life? Or is life an emerging phenomenon resulting from complex chemical reactions, developing networks and cycles until, at a certain critical size of this network, life starts as an emerging property (5)? Within this approach, life is a dynamical system where signal to noise is just marginal; a living system positions itself at the edge of chaos. Finally the only generally accepted theme is that life is the result of evolution, natural selection, and adaptation (6), a...

show abstract

Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms

Cited by 118 publications

References 9 publications

Enigmatic, ultrasmall, uncultivated Archaea

Enigmatic, ultrasmall, uncultivated Archaea

Sizing up metatranscriptomics

Development of an artificial cell, from self-organization to computation and self-reproduction

Contact Info

Product

Resources

About