1
|
Gong Z, Chen J, Jiao X, Gong H, Pan D, Liu L, Zhang Y, Tan T. Genome-scale metabolic network models for industrial microorganisms metabolic engineering: Current advances and future prospects. Biotechnol Adv 2024; 72:108319. [PMID: 38280495 DOI: 10.1016/j.biotechadv.2024.108319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
The construction of high-performance microbial cell factories (MCFs) is the centerpiece of biomanufacturing. However, the complex metabolic regulatory network of microorganisms poses great challenges for the efficient design and construction of MCFs. The genome-scale metabolic network models (GSMs) can systematically simulate the metabolic regulation process of microorganisms in silico, providing effective guidance for the rapid design and construction of MCFs. In this review, we summarized the development status of 16 important industrial microbial GSMs, and further outline the technologies or methods that continuously promote high-quality GSMs construction from five aspects: I) Databases and modeling tools facilitate GSMs reconstruction; II) evolving gap-filling technologies; III) constraint-based model reconstruction; IV) advances in algorithms; and V) developed visualization tools. In addition, we also summarized the applications of GSMs in guiding metabolic engineering from four aspects: I) exploring and explaining metabolic features; II) predicting the effects of genetic perturbations on metabolism; III) predicting the optimal phenotype; IV) guiding cell factories construction in practical experiment. Finally, we discussed the development of GSMs, aiming to provide a reference for efficiently reconstructing GSMs and guiding metabolic engineering.
Collapse
Affiliation(s)
- Zhijin Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiayao Chen
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinyu Jiao
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Danzi Pan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingli Liu
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yang Zhang
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
2
|
Han YS, Barillas-Mury C. Implications of Time Bomb model of ookinete invasion of midgut cells. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2002; 32:1311-1316. [PMID: 12225921 DOI: 10.1016/s0965-1748(02)00093-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this review, we describe the experimental observations that led us to propose the Time Bomb model of ookinete midgut invasion and discuss potential implications of this model when considering malaria transmission-blocking strategies aimed at arresting parasite development within midgut cells. A detailed analysis of the molecular interactions between Anopheles stephensi midgut epithelial cells and Plasmodium berghei parasites, as they migrate through midgut cells, revealed that ookinetes induce nitric oxide synthase (NOS) expression, remodeling of the actin cytoskeleton and characteristic morphological changes in the invaded epithelial cells. Parasites inflict extensive damage that ultimately leads to genome fragmentation and cell death. During their migration through the cytoplasm, ookinetes release a subtilisin-like protease (PbSub2) and the surface protein (Pbs21). The model proposes that ookinetes must escape rapidly from the invaded cells, as the responses mediating cell death could be potentially lethal to the parasites. In other words, the physical and/or chemical damage triggered by the parasite can be thought of as a 'lethal bomb'. Once this cascade of events is initiated, the parasite must leave the cellular compartment within a limited time to escape unharmed from the 'bomb' it has activated. The midgut epithelium has the ability to heal rapidly by 'budding off' the damaged cells to the midgut lumen without losing its integrity.
Collapse
Affiliation(s)
- Yeon Soo Han
- Department of Microbiology, Immunology and Pathology, Colorado State University, 300 West Lake Street, Fort Collins, CO 80523, USA
| | | |
Collapse
|
3
|
Severson DW, Brown SE, Knudson DL. Genetic and physical mapping in mosquitoes: molecular approaches. ANNUAL REVIEW OF ENTOMOLOGY 2001; 46:183-219. [PMID: 11112168 DOI: 10.1146/annurev.ento.46.1.183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The genetic background of individual mosquito species and populations within those species influences the transmission of mosquito-borne pathogens to humans. Technical advances in contemporary genomics are contributing significantly to the detailed genetic analysis of this mosquito-pathogen interaction as well as all other aspects of mosquito biology, ecology, and evolution. A variety of DNA-based marker types are being used to develop genetic maps for a number of mosquito species. Complex phenotypic traits such as vector competence are being dissected into their discrete genetic components, with the intention of eventually using this information to develop new methods to prevent disease transmission. Both genetic- and physical-mapping techniques are being used to define and compare genome architecture among and within mosquito species. The integration of genetic- and physical-map information is providing a sound framework for map-based positional cloning of target genes of interest. This review focuses on advances in genome-based analysis and their specific applications to mosquitoes.
Collapse
Affiliation(s)
- D W Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA.
| | | | | |
Collapse
|
4
|
Beard CB, Durvasula RV, Richards FF. Bacterial symbiosis in arthropods and the control of disease transmission. Emerg Infect Dis 1998; 4:581-91. [PMID: 9866734 PMCID: PMC2640264 DOI: 10.3201/eid0404.980408] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bacterial symbionts may be used as vehicles for expressing foreign genes in arthropods. Expression of selected genes can render an arthropod incapable of transmitting a second microorganism that is pathogenic for humans and is an alternative approach to the control of arthropod-borne diseases. We discuss the rationale for this alternative approach, its potential applications and limitations, and the regulatory concerns that may arise from its use in interrupting disease transmission in humans and animals.
Collapse
Affiliation(s)
- C B Beard
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
| | | | | |
Collapse
|
5
|
Baldridge GD, Fallon AM. Evidence for DNA endonuclease activity in nuclear extracts from mosquito cells. Comp Biochem Physiol B Biochem Mol Biol 1995; 110:17-32. [PMID: 7858941 DOI: 10.1016/0305-0491(94)00144-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We describe a deoxyribonuclease activity from nuclear protein extracts of cultured Aedes albopictus mosquito cells. The nuclease cleaved linear and circular double-stranded DNA, first generating 3' OH single-stranded nicks followed by second strand cleavage, but had little or no exonucleolytic activity. Detection of this activity was optimal at pH 7.1, in the presence of a divalent cation (Mg2+, Ca2+, Mn2+, Ba2+). In the presence of Mg2+, Zn2+, Hg2+ and Cu2+ inhibited activity, sulfhydryl reagents and ATP had no effect. At physiological temperatures (18-35 degrees C), linear double-stranded DNA probes were preferentially cleaved near sites containing 3-6 consecutive deoxyadenine/thymine base pairs. Results from salt dependency and drug inhibition studies, combined with inspection of DNA sequence, suggested that DNA structure is among the parameters that determine preferred cleavage sites.
Collapse
Affiliation(s)
- G D Baldridge
- Department of Entomology, University of Minnesota, St Paul 55108
| | | |
Collapse
|
6
|
Hill SM, Crampton JM. DNA-based methods for the identification of insect vectors. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 1994; 88:227-50. [PMID: 7944669 DOI: 10.1080/00034983.1994.11812864] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Many insect vectors are members of complexes composed of morphologically identical sibling species. The identification of individual species, a requirement of epidemiological studies and control programmes, has traditionally relied upon techniques such as chromosomal analysis or isoenzyme typing. Owing to the limitations of these techniques, the last few years have seen many developments in DNA-based technologies for identification. DNA-based protocols have advantages over the other techniques utilized, in that they may identify all insect stages of both sexes using alcohol-preserved, dried, fresh or frozen specimens. The methods ultimately rely upon either DNA probe hybridization or the polymerase chain reaction (PCR). This review describes a number of approaches taken towards the development of these techniques. The aim of these approaches, whether directed or random, is to produce a methodology that is cheap, accurate and easy to use. In this review, the DNA-based techniques developed for the identification of Anopheles gambiae complex mosquitoes are used to illustrate the power of these methods, although, as the review demonstrates, the technology is directly applicable to many other mosquito or insect vectors. In addition, the methods discussed may be utilized for generating additional epidemiological data, such as identification of parasites within the vector or origin of the bloodmeal. A comprehensive survey of the probe systems available for the identification of insect vectors and the disease-causing organisms they transmit to the human population is therefore included. Given further advances in this technology, it may be anticipated that DNA-based approaches to identification may eventually supersede more traditional methodologies in the fields of tropical medicine and parasitology.
Collapse
Affiliation(s)
- S M Hill
- Wolfson Unit of Molecular Genetics, School of Tropical Medicine, Liverpool, U.K
| | | |
Collapse
|
7
|
Severson DW, Mori A, Zhang Y, Christensen BM. Chromosomal mapping of two loci affecting filarial worm susceptibility in Aedes aegypti. INSECT MOLECULAR BIOLOGY 1994; 3:67-72. [PMID: 7987523 DOI: 10.1111/j.1365-2583.1994.tb00153.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two quantitative trait loci (QTL) affecting susceptibility of the mosquito Aedes aegypti to the filarial worm parasite Brugia malayi were identified using restriction fragment length polymorphism (RFLP) markers. The first locus, fsb[1,LF178], resides within a 10 cM interval on chromosome 1 and exhibits a recessive effect with respect to susceptibility. The second locus, fsb[2,LF98], resides within a 9 cM interval on chromosome 2 and exhibits an additive effect on susceptibility. Significant epistasis was detected between these loci, although the effect of fsb[2,LF98] was dependent on the genetic background of the mosquito strains. Suggestions for a standard QTL nomenclature are included.
Collapse
Affiliation(s)
- D W Severson
- Department of Animal Health and Biomedical Sciences, University of Wisconsin, Madison 53706
| | | | | | | |
Collapse
|
8
|
Salazar CE, Hamm DM, Wesson DM, Beard CB, Kumar V, Collins FH. A cytoskeletal actin gene in the mosquito Anopheles gambiae. INSECT MOLECULAR BIOLOGY 1994; 3:1-13. [PMID: 8069411 DOI: 10.1111/j.1365-2583.1994.tb00145.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Five actin genes have been identified in the mosquito Anopheles gambiae, and a constitutively expressed actin gene has been chosen for detailed analysis. We have physically mapped and sequenced this gene and six associated cDNAs, including translated coding regions, as well as the 5' and 3' flanking sequences. Analysis of stage-specific RNA shows this gene to be present in all stages of mosquito development and in an established A. gambiae cell line, thus indicating a cytoskeletal actin. In the sequence of the translated coding region and in pattern of expression, this gene is very similar to the cytoskeletal actin genes of Drosophila melanogaster, and in sequence, equally similar to the Artemia cytoskeletal actin gene 403 (99.2% identity among the three amino acid sequences). Sequencing of this A. gambiae actin gene (designated act1D for its location in chromosome division 1D) and selected cDNAs shows that it possesses three alternative leader sequences; thus the gene appears to have three alternative promoters. These promoters should ultimately prove useful in the production of transgenic constructs for constitutive expression.
Collapse
Affiliation(s)
- C E Salazar
- Department of Biology, Emory University, Atlanta, Georgia
| | | | | | | | | | | |
Collapse
|
9
|
|
10
|
Severson DW. Applications of molecular marker analysis to mosquito vector competence. ACTA ACUST UNITED AC 1994; 10:336-40. [PMID: 15275410 DOI: 10.1016/0169-4758(94)90243-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A rapidly expanding cadre of molecular biology techniques is being developed for human and plant genetics, including development of the technology to identify large numbers of genetic markers and to evaluate these markers relative to phenotypic observations. In this review, David Severson discusses applications of these techniques for the analysis of mosquito vector competence.
Collapse
Affiliation(s)
- D W Severson
- Department of Animal Health and Biomedical Sciences, 1655 Linden Drive, University of Madison, Madison, WI 53706, USA
| |
Collapse
|
11
|
Kumar A, Rai KS. Molecular organization and evolution of mosquito genomes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1993; 106:495-504. [PMID: 7904233 DOI: 10.1016/0305-0491(93)90123-m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Given the importance of mosquitoes as disease vectors, relatively little is known about the molecular organization and evolution of mosquito genomes as compared to other insects such as fruit flies. The advances in recombinant DNA technology and the possibility that mosquito populations could be controlled and genetically manipulated using such technology has stimulated considerable research during the last few years in the areas of genome organization and evolution, genome mapping, endogenous transposable elements, and mapping and characterization of genes conferring susceptibility to different parasites and pathogens. This review summarizes research currently underway in our laboratory and elsewhere in these areas.
Collapse
Affiliation(s)
- A Kumar
- Department of Biological Sciences, University of Notre Dame, IN 46556
| | | |
Collapse
|
12
|
Besansky NJ, Finnerty V, Collins FH. Molecular Perspectives on the Genetics of Mosquitoes. ADVANCES IN GENETICS 1992; 30:123-84. [PMID: 1360745 DOI: 10.1016/s0065-2660(08)60320-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- N J Besansky
- Malaria Branch, Centers for Disease Control, Atlanta, Georgia 30333
| | | | | |
Collapse
|