Bacteria 3D genomics

Bacteria, the most widely distributed species on Earth, play an important role in the biosphere and in human life. Unlike eukaryotes, bacteria do not have a nucleus, and most of the bacterial genetic materials are concentrated in a specific area of the cell, known as the nucleoid. Bacterial cells vary in morphology and are rich in genetic diversity. However, until now, little is known about the way in which bacterial chromosomes are organized. Are the chromosomes in the bacteria randomly distributed or are there specific organization patterns? With the rise of genome sequencing technology, more and more regulatory elements in bacteria have been resolved. The one-dimensional organization pattern of the bacterial genome has gradually become clear. There are several sets of evidence that the genome layout is not random. The chromosome conformation capture and super-resolution microscopy technology developed in recent years provide a powerful tool for the study of bacterial three-dimensional genomes; the former is often a high-throughput method using cell populations as experimental materials, while the latter is low-throughput method based on single-cell molecular markers; these two methods are usually used in conjunction with each other. The sequencing data obtained by 3C/Hi-C technology can be processed in common pipelines like eukaryotes. In recent years, some software tools for constructing the three-dimensional structures of chromosomes based on 3C/Hi-C data have appeared, but they are usually aimed at eukaryotic species, and tools for prokaryotes have yet to be developed. At present, five bacterial model species, namely, Caulobacter crescentus, Escherichia coli, Bacillus subtilis, Vibrio cholerae, Mycoplasma pneumoniae, have undergone preliminary three-dimensional genome research, and some knowledge about the spatial organization characteristics of bacterial chromosomes has been obtained, revealing the important roles of nucleoid-associated proteins in chromosomal spatial organization. It was found that bacterial chromosomal spatial organization is connected with gene transcription and cell cycles, which has greatly extended our knowledge on the three-dimensional genome of bacteria. However, compared with eukaryotes, the research on the three-dimensional genome of prokaryotes is still insufficient. In view of the complexity of biological processes, the spatial structure of bacterial chromosome is correlated with intracellular and external signal stimulation responses, gene expression regulation, protein interactions, and metabolic processes. Understanding the physiological functions of bacterial three-dimensional genomes from a systematic perspective will be the research focus in future.